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				<h1 class="firstHeading">Installation Guide</h1>
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			<p><big> <b>Instructions for installing BioNetGen2</b></big>
</p>
<table id="toc" class="toc" summary="Contents"><tr><td><div id="toctitle"><h2>Contents</h2></div>
<ul>
<li class='toclevel-1'><a href="#Requirements"><span class="tocnumber">1</span> <span class="toctext">Requirements</span></a></li>
<li class='toclevel-1'><a href="#Install_the_BioNetGen_source_code"><span class="tocnumber">2</span> <span class="toctext">Install the BioNetGen source code</span></a></li>
<li class='toclevel-1'><a href="#Install_the_simulation_back_end"><span class="tocnumber">3</span> <span class="toctext">Install the simulation back end</span></a>
<ul>
<li class='toclevel-2'><a href="#Downloading_the_pre-compiled_binary"><span class="tocnumber">3.1</span> <span class="toctext">Downloading the pre-compiled binary</span></a></li>
<li class='toclevel-2'><a href="#Compiling_from_source"><span class="tocnumber">3.2</span> <span class="toctext">Compiling from source</span></a></li>
</ul>
</li>
<li class='toclevel-1'><a href="#Test_run"><span class="tocnumber">4</span> <span class="toctext">Test run</span></a></li>
<li class='toclevel-1'><a href="#Validation"><span class="tocnumber">5</span> <span class="toctext">Validation</span></a></li>
<li class='toclevel-1'><a href="#Getting_Started"><span class="tocnumber">6</span> <span class="toctext">Getting Started</span></a></li>
</ul>
</td></tr></table><script type="text/javascript"> if (window.showTocToggle) { var tocShowText = "show"; var tocHideText = "hide"; showTocToggle(); } </script>
<div class="editsection" style="float:right;margin-left:5px;">[<a href="/BioNetWiki/index.php?title=Installation_Guide&amp;action=edit&amp;section=1" title="Edit section: Requirements">edit</a>]</div><a name="Requirements"></a><h2>Requirements</h2>
<p>BioNetGen2 is written in the Perl language.  The simulation back end, run_network, is written in C.  The RuleBuilder front end, which is optional, is written in Java.
</p><p>Running BioNetGen requires
</p>
<ul><li> Perl version 5.8 or above
</li></ul>
<p>Compiling run_network requires
</p>
<ul><li> gcc and make
</li></ul>
<p>Pre-compiled binaries are provided for Linux, MacOSX, and Windows.
</p><p>Running RuleBuilder requires
</p>
<ul><li> Java 1.5.0 Runtime Environment or above
</li></ul>
<p>Accessing network generation and simulation capabilities from RuleBuilder also requires that BioNetGen and run_network are installed.
</p>
<div class="editsection" style="float:right;margin-left:5px;">[<a href="/BioNetWiki/index.php?title=Installation_Guide&amp;action=edit&amp;section=2" title="Edit section: Install the BioNetGen source code">edit</a>]</div><a name="Install_the_BioNetGen_source_code"></a><h2>Install the BioNetGen source code</h2>
<ul><li> Obtain the latest source distribution from the <a href="http://cellsignaling.lanl.gov/BioNetGen2/Downloads/Source" class='external text' title="http://cellsignaling.lanl.gov/BioNetGen2/Downloads/Source" rel="nofollow">download directory</a>. You will be prompted for a username, which is BNG2, and a password, which is rulebuilder. The source distribution file is BioNetGen_x.xx.xxx.tgz. 
</li><li> Place the source distribution file in the location where your would like to install BioNetGen2.
</li><li> Unzip the source by typing 'tar xvzf &lt;file&gt;.tgz', where file is the name of the BioNetGen2 source file.
</li></ul>
<div class="editsection" style="float:right;margin-left:5px;">[<a href="/BioNetWiki/index.php?title=Installation_Guide&amp;action=edit&amp;section=3" title="Edit section: Install the simulation back end">edit</a>]</div><a name="Install_the_simulation_back_end"></a><h2>Install the simulation back end</h2>
<p>There are two options - 1) Download a precompiled binary from the website for
your operating system, if its available, 2) Compile the binary from source.
</p>
<div class="editsection" style="float:right;margin-left:5px;">[<a href="/BioNetWiki/index.php?title=Installation_Guide&amp;action=edit&amp;section=4" title="Edit section: Downloading the pre-compiled binary">edit</a>]</div><a name="Downloading_the_pre-compiled_binary"></a><h3>Downloading the pre-compiled binary</h3>
<p>Pre-compiled versions of the simulation back end are available for <a href="http://cellsignaling.lanl.gov/BioNetGen2/Downloads/Binaries" class='external text' title="http://cellsignaling.lanl.gov/BioNetGen2/Downloads/Binaries" rel="nofollow">downloading</a>.
Simply extract the archive file in the main BioNetGen directory (BioNetGen_2.x.xx) and proceed to testing.
Click <a href="/BioNetWiki/index.php/Binary_executables" title="Binary executables">here</a> to see platforms for which binaries are available.
</p>
<div class="editsection" style="float:right;margin-left:5px;">[<a href="/BioNetWiki/index.php?title=Installation_Guide&amp;action=edit&amp;section=5" title="Edit section: Compiling from source">edit</a>]</div><a name="Compiling_from_source"></a><h3>Compiling from source</h3>
<p>Prerequisites are a working gcc compiler and the make utility.  These are
usually found on any linux box or Mac with OS X installed, but may need to be
specially installed on a Windows machine.
</p>
<ul><li> cd to the root BioNetGen directory and type 'make'. 
</li><li> The main Makefile and the source code for the back end is in the Network2 directory, in case you encounter any problems.
</li></ul>
<div class="editsection" style="float:right;margin-left:5px;">[<a href="/BioNetWiki/index.php?title=Installation_Guide&amp;action=edit&amp;section=6" title="Edit section: Test run">edit</a>]</div><a name="Test_run"></a><h2>Test run</h2>
<p>The main BioNetGen executable is the Perl script, BNG2.pl in the Perl2
directory.  BNG2 can be run from the command line by typing
</p>
<pre> path-to-Perl2/BNG2.pl file.bngl
</pre>
<p>To test this, cd to the Models2 directory, and type '../Perl2/BNG2.pl
toy-jim.bngl'. You should see some output like
</p>
<pre>
BioNetGen version 2.0.32+
Reading from file toy-jim.bngl
Read 16 parameters.
Read 5 species.
Adding P as allowed state of component Y of molecule K
Read 8 reaction rule(s).
Read 9 observable(s).
WARNING: Removing old network file toy-jim.net.
Iteration   0:     5 species      0 rxns  0.00e+00 CPU s
Iteration   1:     8 species      3 rxns  2.00e-02 CPU s
...
Running run_network on ntal.local
full command: &quot;../bin/run_network&quot; -o &quot;toy-jim_kinetics&quot; -p cvode -a 1e-10 -r 1e-08 -g &quot;toy-jim_kinetics.net&quot; &quot;toy-jim_kinetics.net&quot; 1 120
Read 16 parameters
Read 25 species
Read 101 reaction(s)
...
</pre>
<p>If run_network is able to run, then the compilation has been successful.
</p>
<div class="editsection" style="float:right;margin-left:5px;">[<a href="/BioNetWiki/index.php?title=Installation_Guide&amp;action=edit&amp;section=7" title="Edit section: Validation">edit</a>]</div><a name="Validation"></a><h2>Validation</h2>
<p>To make sure that you have a properly functioning BioNetGen program, cd to the
Validate directory and type 'perl validate_examples.pl'.  This may take a few
minutes to run. The validation suite is currently under construction, so only
a limited subset of BNG features are tested.
</p>
<div class="editsection" style="float:right;margin-left:5px;">[<a href="/BioNetWiki/index.php?title=Installation_Guide&amp;action=edit&amp;section=8" title="Edit section: Getting Started">edit</a>]</div><a name="Getting_Started"></a><h2>Getting Started </h2>
<p>A tutorial that describes the basic and some advanced features of BioNetGen2
is available in the Tutorial directory.  We are working on getting this into
an online wiki format, to improve the formatting and coverage.
</p><p><br />
RuleBuilder provides a graphical user interface to BioNetGen. With the Java Runtime Environment installed, it can be run either by double-clicking on the RuleBuilder-x.xx.jar file in the RuleBuilder directory, or typing
</p>
<pre>&gt; java -jar RuleBuilder-x.xx.jar
</pre>
<p>from the command line.  Additional intstructions for configuring and running RuleBuilder are provided in the INSTALL_RB.pdf and the RuleBuilder_GettingStarted.pdf files in the RuleBuilder directory.
</p>
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